Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking
Sikdar, Sinjini ; Joehanes, Roby ; Joubert, Bonnie R. ; Xu, Cheng Jian ; Vives-Usano, Marta ; Rezwan, Faisal I. ; Felix, Janine F. ; Ward, James M. ; Guan, Weihua ; Richmond, Rebecca C. ; Brody, Jennifer A. ; Küpers, Leanne K. ; Baïz, Nour ; Håberg, Siri E. ; Smith, Jennifer A. ; Reese, Sarah E. ; Aslibekyan, Stella ; Hoyo, Cathrine ; Dhingra, Radhika ; Markunas, Christina A. ; Xu, Tao ; Reynolds, Lindsay M. ; Just, Allan C. ; Mandaviya, Pooja R. ; Ghantous, Akram ; Bennett, Brian D. ; Wang, Tianyuan ; Consortium, The Bios ; Bakulski, Kelly M. ; Melen, Erik ; Zhao, Shanshan ; Jin, Jianping ; Herceg, Zdenko ; Meurs, Joyce Van; Taylor, Jack A. ; Baccarelli, Andrea A. ; Murphy, Susan K. ; Liu, Yongmei ; Munthe-Kaas, Monica Cheng ; Deary, Ian J. ; Nystad, Wenche ; Waldenberger, Melanie ; Annesi-Maesano, Isabella ; Conneely, Karen ; Jaddoe, Vincent W.V. ; Arnett, Donna ; Snieder, Harold ; Kardia, Sharon L.R. ; Relton, Caroline L. ; Ong, Ken K. ; Ewart, Susan ; Moreno-Macias, Hortensia ; Romieu, Isabelle ; Sotoodehnia, Nona ; Fornage, Myriam ; Motsinger-Reif, Alison ; Koppelman, Gerard H. ; Bustamante, Mariona ; Levy, Daniel ; London, Stephanie J. - \ 2019
Epigenomics 11 (2019)13. - ISSN 1750-1911 - p. 1487 - 1500.
cigarette smoking - epigenetics - infant - maternal exposure - methylation

Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.

Improving scientific advice for the conservation and management of oceanic sharks and rays : Final report - Study
Coelho, R. ; Apostolaki, P. ; Bach, P. ; Brunel, T.P.A. ; Davies, T. ; Diez, G. ; Ellis, J. ; Escalle, L. ; Lopez, J. ; Merino, Gorka ; Mitchell, R. ; Macias, D. ; Murua, H. ; Overzee, H.M.J. van; Poos, J.J. ; Richardson, H. ; Rosa, D. ; Sanchez, S. ; Santos, C. ; Seret, B. ; Urbina, J.O. ; Walker, N. - \ 2019
Brussels : European Commission - ISBN 9789292024550 - 658 p.
The purpose of this specific study is to provide the Directorate-General for Maritime Affairs and Fisheries (DG MARE) with: Updated information regarding the association or occurrence of pelagic sharks and rays in different fisheries; Updated information regarding data collection and methodological approaches for the assessment of conservation status of sharks; A critical review of existing Conservation and Management Measures (CMMs) for sharks and of the current conservation status of the species concerned; and Proposals to improve and/or provide alternative options for conservation and management of sharks taking into account any recent methodological advances and new data or information. The species of interest are the main pelagic sharks caught by pelagic fisheries, including under Sustainable Fisheries Partnership Agreements (longline and purse seine fisheries). The study also considers some pelagic elasmobranchs included in Article 13 (species prohibitions) of the Council Regulation 2016/72 fixing for 2016 the fishing opportunities for certain fish stocks. The main regions focused are the oceanic regions covered by tuna-RFMOs where those species of elasmobranch are represented in the catches, specifically the Atlantic (ICCAT region), the Indian Ocean (IOTC region) and the Pacific (WCPFC and IATTC regions)
Publisher Correction to : Background invertebrate herbivory on dwarf birch (Betula glandulosa-nana complex) increases with temperature and precipitation across the tundra biome
Barrio, Isabel C. ; Lindén, Elin ; Beest, Mariska Te; Olofsson, Johan ; Rocha, Adrian ; Soininen, Eeva M. ; Alatalo, Juha M. ; Andersson, Tommi ; Asmus, Ashley ; Boike, Julia ; Bråthen, Kari Anne ; Bryant, John P. ; Buchwal, Agata ; Bueno, C.G. ; Christie, Katherine S. ; Egelkraut, Dagmar ; Ehrich, Dorothee ; Fishback, Lee Ann ; Forbes, Bruce C. ; Gartzia, Maite ; Grogan, Paul ; Hallinger, Martin ; Heijmans, Monique M.P.D. ; Hik, David S. ; Hofgaard, Annika ; Holmgren, Milena ; Høye, Toke T. ; Huebner, Diane C. ; Jónsdóttir, Ingibjörg Svala ; Kaarlejärvi, Elina ; Kumpula, Timo ; Lange, Cynthia Y.M.J.G. ; Lange, Jelena ; Lévesque, Esther ; Limpens, Juul ; Macias-Fauria, Marc ; Myers-Smith, Isla ; Nieukerken, Erik J. van; Normand, Signe ; Post, Eric S. ; Schmidt, Niels Martin ; Sitters, Judith ; Skoracka, Anna ; Sokolov, Alexander ; Sokolova, Natalya ; Speed, James D.M. ; Street, Lorna E. ; Sundqvist, Maja K. ; Suominen, Otso ; Tananaev, Nikita ; Tremblay, Jean Pierre ; Urbanowicz, Christine ; Uvarov, Sergey A. ; Watts, David ; Wilmking, Martin ; Wookey, Philip A. ; Zimmermann, Heike H. ; Zverev, Vitali ; Kozlov, Mikhail V. - \ 2018
Polar Biology 41 (2018)8. - ISSN 0722-4060 - p. 1653 - 1654.
The above mentioned article was originally scheduled for publication in the special issue on Ecology of Tundra Arthropods with guest editors Toke T. Høye . Lauren E. Culler. Erroneously, the article was published in Polar Biology, Volume 40, Issue 11, November, 2017. The publisher sincerely apologizes to the guest editors and the authors for the inconvenience caused.
Automated assembly of species metabolomes through data submission into a public repository
Salek, Reza ; Conesa, Pablo ; Cochrane, Keeva ; Haug, Kenneth ; Williams, M. ; Kale, Namrata ; Moreno, P. ; Jayaseelan, Kalai Vanii ; Macias, Jose Ramon ; Nainala, Venkata Chandrasekhar ; Hall, R.D. ; Reed, Laura ; Viant, Mark ; Donovan, C. ; Steinbeck, Christoph - \ 2017
GigaScience 6 (2017)8. - ISSN 2047-217X - 4 p.
Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.
Comparing NaOH-extractable organic matter of acid forest soils that differ in their pedogenic trends: a pyrolysis-GC/MS study
Suarez Abelenda, M. ; Buurman, P. ; Camps Arbestain, M. ; Kaal, J. ; Martinez-Cortizas, A. ; Gartzia-Bengoetxea, N. ; Macias, F. - \ 2011
European Journal of Soil Science 62 (2011)6. - ISSN 1351-0754 - p. 834 - 848.
chromatography-mass-spectrometry - gas-chromatography - chemical-composition - humic acids - fractions - peat - chemistry - horizons - aluminum - andosols
Soil organic matter (SOM) in Alu-andic Andosols and Alu-humic Umbrisols is believed to accumulate because of the protection caused by binding to aluminium (Al). We investigated soils that differed in the abundance of organo-Al complexes to determine the effect of such binding on SOM chemistry. For this, the surface horizons of three types of acid soils in the Basque Country (northern Spain) under forest stands were studied: (i) Alu-andic Andosols (AND soils) on basalts and trachytes, (ii) Umbrisols or so-called ‘aluminic’(ALU) soils also on basalts and trachytes and (iii) soils with a podzolizing trend (POD), on quartzites. Values of Al extractable with sodium pyrophosphate (Alp) in the surface horizons of these soils ranged between 8.5 and 13.1, 1.9 and 9.3, and 0.8 and 3.7 g kg-1 dry weight, for the AND, ALU and POD soils respectively. For POD and ALU soils, surface horizons were sampled at two depths, 0–5 and 5–20 cm, whereas the AND soils were sampled at different depths down to the B horizon. NaOH-extractable SOM from three AND soils, 12 ALU soils and 12 POD soils was studied by pyrolysis-gas chromatography/mass spectrometry. The POD soils had the largest loads of plant-derived markers (lignin, long-chain alkanes and alkenes, methyl ketones, fatty acids); SOM of the AND soils had the smallest amounts of plant-derived SOM and the largest amounts of microbial products (microbial sugars and N-compounds) of the soils studied. ALU soils had an intermediate pattern, as expected. The results indicate that the SOM of Alu-andic Andosols, developed from basalt and trachyte rocks, is essentially dissimilar to that of soils derived from quartz-rich parent material, under the same climate conditions and similar forest stands. The dominance of secondary (microbial-derived) SOM in Alu-andic Andosols, also observed in previous research on Sil-andic Andosols (these are dominated by short-range ordered Si compounds in contrast to the dominance of organo-Al complexes in Alu-andic Andosols), reveals the small contribution of primary (plant-derived) material to SOM in soils with andic properties
Assessment and characterization of the diet of an isolated population in the Bolivian Andes
Berti, P.R. ; Jones, A.D. ; Cruz Agudo, Y. ; Larrea Macias, S. ; Borja, R. ; Sherwood, S.G. - \ 2010
American Journal of Human Biology 22 (2010)6. - ISSN 1042-0533 - p. 741 - 749.
fatty-acids - food - validation - community - children - recall
Objectives: The goal of this research is to characterize the composition and nutrient adequacy of the diets in the northern region of the Department of Potosí, Bolivia. Communities in this semiarid, mountainous region are isolated and impoverished having the highest rates of child malnutrition and under-five mortality in the Americas. Methods: A total of 2,222 twenty-four-hour dietary recalls were conducted in 30 communities during May and November 2006 and May and November 2007. Food composition data were compiled from diverse published sources and integrated with the recall data to estimate intakes of energy, protein, fat, carbohydrates, and seven micronutrients. Diets were characterized in terms of food sources, seasonality, and nutrient adequacy. Results: The diet relies heavily on the potato and other tubers (54% of dietary energy) and grains (30% of dietary energy). Although crop production is seasonal, off-season consumption of chuño helps to minimize seasonal fluctuations in dietary energy intake. Despite relative monotony, intakes of iron, vitamin C, most B vitamins, and vitamin A in adults are probably adequate; riboflavin, calcium, and vitamin A intakes in children are low. Nevertheless, extremely low dietary fat intakes (approximately 3–9% of dietary energy from fat) likely prevent adequate absorption of fat-soluble vitamins as well as lead to deficiencies of essential fatty acids. Conclusions: Dietary inadequacies, especially of fats, may explain much of the poor health observed in northern Potosí. An improved diet may be possible through increasing production and intake of local fat-rich food sources such as small animals. Am. J. Hum. Biol., 2010. © 2010 Wiley-Liss, Inc.
Pyrolysis-gas chromatography/mass spectrometry of soil organic matter extracted from a Brazilian mangrove and Spanish salt marshes
Perobelli Ferreira, F. ; Buurman, P. ; Macias, F. ; Otero, X.L. ; Boluda, R. - \ 2009
Soil Science Society of America Journal 73 (2009). - ISSN 0361-5995 - p. 841 - 851.
rothamsted classical experiments - particle-size fractions - humic substances - mass-spectrometry - chemical characterization - vegetation succession - molecular composition - sao-paulo - nw spain - acids
The soil organic matter (SOM) extracted under different vegetation types from a Brazilian mangrove (Pai Matos Island, São Paulo State) and from three Spanish salt marshes (Betanzos Ría and Corrubedo Natural Parks, Galícia, and the Albufera Natural Park, Valencia) was investigated by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). The chemical variation was larger in SOM from the Spanish marshes than in the SOM of the Brazilian mangroves, possibly because the marshes included sites with both tidal and nontidal variation, whereas the mangrove forest underwent just tidal variation. Thus, plant-derived organic matter was better preserved under permanently anoxic environments. Moreover, given the low number of studied profiles and sedimentary¿vegetation sequences in both areas, depth trends remain unclear. The chemical data also allow distinction between the contributions of woody and nonwoody vegetation inputs. Soil organic matter decomposition was found to cause: (i) a decrease in lignin contents and a relative increase in aliphatics; (ii) an increase in short-chain aliphatics at the expense of longer ones; (iii) a loss of odd-over-even dominance in alkanes and alkenes; and (iv) an increase in microbial products, including proteins, sterols, short-chain fatty acids, and alkanes. Pyrolysis-gas chromatography/mass spectrometry is a useful tool to study the behavior and composition of SOM in wetland environments such as mangroves and salt marshes. Additional profiles need to be studied for each vegetation type, however, to improve the interpretability of the chemical data
NaOH-extractable organic matter of andic soils from Galicia (NW Spain) under different land use regimes: a pyrolysis GC/MS study
Verde, J.R. ; Buurman, P. ; Martinez-Cortizas, A. ; Macias, F. ; Camps Arbestain, M. - \ 2008
European Journal of Soil Science 59 (2008)6. - ISSN 1351-0754 - p. 1096 - 1110.
polycyclic aromatic-hydrocarbons - ionization mass-spectrometry - volcanic ash soils - gas chromatography - humic substances - forest soil - acids - carbon - decomposition - preservation
The objective of this study was to determine to what extent the attenuation or loss of andic soil properties caused by land use change ¿ from forest (FOR, average C content 118.2 ± 23.7 g kg¿1) to agricultural land (AGR, average C content 55.7 ± 16.7 g kg¿1) use ¿ is reflected in soil organic matter (SOM) at the molecular level. For this, NaOH-extractable SOM of A horizons from 17 soils developed on amphibolitic parent material in NW Spain was studied by pyrolysis gas chromatography spectrometry (Py-GC/MS). We also included two buried andic A horizons (PAL, 2200 cal yr BP in age) on the same parent material, as a reference for the molecular composition of SOM from soils without recent litter additions. Organic matter of PAL soils had a composition largely different from that of superficial soils (FOR and AGR), with an important relative contribution of microbial polysaccharides and N-compounds, and an absence of compounds that characterize fresh plant litter (e.g. lignins). In the superficial soils, the relative contribution of lignin-derived compounds was greater in AGR than in FOR soils. Differences were also observed in the relative contribution of aliphatic compounds, FOR soils being enriched in this type of components compared with AGR soils. The results indicated that land use change from FOR to AGR, which was accompanied by a decrease in total SOM, resulted in an enrichment in primary SOM. The smaller relative abundance of primary SOM derivatives in andic FOR soils indicates that these compounds were quickly degraded in Andisols
The allelopathic effect of dead and living mulches from perennial ryegrass (Lolium perenne L.) on Calystegia sepium (L.) R. Br
Hanwen Wu, ; Naber, H. ; Oomen, G.J.M. - \ 1999
In: Recent Advances in Allelopathy / Macias, F.A., Galindo, J.C.G., Molinillo, J.M.G., Cutler, H.G., - p. 351 - 362.
Processos de alteracion y neoformacion mineral en medios derpentinicos de Galicia. Weathering processes and mineral neoformation at serpentinite areas from Gal.
Calvo, R. ; Macias, F. ; Buurman, P. - \ 1987
Cuaderno do Laboratorio Xeoloxico de Laxe 11 (1987). - p. 161 - 170.
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